In 1995, all 800 habitants of the isolated Kamikakushi Island vanished in one night, all but a single girl who lost her memory. The cause of the disappearances was never identified.

Four years later, that girl, Mari, transfers to a girl`s dormitory school, Kaihou Gakuen, leaving behind her grandmother who had been her guardian ever since the incident. There, she meets Hagino.

Hagino is the school idol and completes her student council responsibilities flawlessly. The moment she touches Mari’s hand, however, Hagino freaks out, straddling atop Mari, hands aroundher throat. Mari is afraid of and angry at Hagino, who pretends as if nothing had happened while in front of other students, but at the same time, somehow, she is attracted to Hagino too.

In reality, Hagino is actually an alien who was sent to Earth in order to reconnoiter prior to an invasion. The event on Kamikakushi Island occurred when the 200-member crew of a battleship, the Blue, whose captain was Hagino and the island`s inhabitants had killed each other. The Blue was seriously damaged and hidden. Hagino had since blended into human society and continued her reconnaissance.

Within her school life, while fighting with fellow students, Mari begins to come out of her shell. Hagino has been living a double life, but her encounter with Mari makes her face human beings, and gradually she begins to have doubts about her mission. While the invasion and war draws closer unnoticed, the girls begin to understand each other. (by AnimeNfo.com)

The war against the Arume is set from 2000 to 2008, ending with the aliens winning the conflict.[2] In 2009 the aliens take control of the Japanese government, which sets the backstory for the Blue Drop storylines.[2]

The desicive factor in the Arume's victory was the use of biological weapons and a modified vesion of an alien toy called "emul force" (エミル フォース, emiru fōsu?).[4][5] Along the years, the remnants of this weaponry has become dangerous creatures which the government (ran by the aliens) has to deal with.[4] This is the main premise of the original Blue Drop manga, which is set around a thousand years after the war.[2] The military uses an experimental vaccine that gives human children special abilities for a determined period of time. During this time the military forces them to confront the weapon remnants, an action that usually ends up in the children's death. Most of the chapters follow the conflict between the military and the resistance, which tries to save those who have been given the vaccine, as well as the relationships between the people involved. In addition, the story explores the aliens' traits and behaviour. All of them have blue eyes and can manipulate "emul force", but their main characteristic lies in their gender: they are all female, and their sexual orientation is homosexual.[4]
The aliens' sexual behaviour is dealt with even more prominently (and explicitly) in the Blue Drop: Tenshi no Bokura manga, which shows its consequences upon the human social estructure.[3] This manga also deals with the first experiments done on human beings by the aliens;[2] specifically experiments concerning sex change.[6] Set one year after the war,[2] it focuses in the relationship between Shōta, a normal high-school student, and Kenzō, Shōta's former-male best friend who has been turned into a girl by the aliens.[6]

Unlike both manga stories, the Blue Drop: Tenshitachi no Gikyoku anime series is set before the war.[2] The storyline starts in 1999, with Mari Wakatake transfering to a girl's dormitory school called Kaihō Academy (海凰学園, Kaihō Gakuen?).[2] Mari's background hides a traumatic past: four years before her arrival at Kaihō, all the inhabitants of the island where she lived died in one night. Mari was the only survivor, but lost all her memories prior that point.
At the academy Mari meets Hagino Senkōji, the school idol and class rep. Although Hagino is introduced as a calm and collected person, when she touches Mari's hand the viewer sees her freaking out and trying to strangle Mari. From then on, Mari is torn between anger and attraction towards Hagino, who pretends as if nothing had happened.[7]
Unbeknown to Mari, Hagino is actually the captain of an alien battleship called Blue, which is the vanguard of the invasion to Earth. The incident on the island where Mari lived occurred when the crew of the ship and the island's inhabitants killed each other. The Blue was seriously damaged and hidden, and Hagino blended into human society and continued her reconnaissance.
The story focuses on the relationship between Mari and Hagino;[7] as Mari begins to come out of her shell, Hagino, who has been living a double life, gradually begins to have doubts about her mission. While the invasion and war draw closer unnoticed, they begin to understand each other.